I was in the same shoes last week. Yes it is very unclear how it will work so I applied before June 30 to old reg board in NSW for reinstatement (had previously been registered) under the TTMR. I decided to this just in case there were any problems.
You now have to apply through the new National board. However when I was enquiring the NSW board said the TTMR would still apply with the new board. And from the NZ perspective I asked both the NZ physio board and the NZSP if there has been any indication that Australia was dropping the TTMR. They said they had not had had any discussions of this and as this would be a major change in direction, and would ruffle a lot of feathers if Australia violated the agreement it seems highly unlikely.
The new board doesn't seem to be very sorted - very unclear of what it is doing at this late stage. I would therefore get directly in contact with the Aust Physio Board and get them to clarify what you need to do